Suppr超能文献

基于机器学习的虚拟筛选探索红树林天然产物作为KRAS抑制剂。

Virtual Screening Based on Machine Learning Explores Mangrove Natural Products as KRAS Inhibitors.

作者信息

Luo Lianxiang, Zheng Tongyu, Wang Qu, Liao Yingling, Zheng Xiaoqi, Zhong Ai, Huang Zunnan, Luo Hui

机构信息

The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China.

The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China.

出版信息

Pharmaceuticals (Basel). 2022 May 8;15(5):584. doi: 10.3390/ph15050584.

Abstract

Mangrove secondary metabolites have many unique biological activities. We identified lead compounds among them that might target KRAS KRAS is considered to be closely related to various cancers. A variety of novel small molecules that directly target KRAS are being developed, including covalent allosteric inhibitors for KRAS mutant, protein-protein interaction inhibitors that bind in the switch I/II pocket or the A59 site, and GTP-competitive inhibitors targeting the nucleotide-binding site. To identify a candidate pool of mangrove secondary metabolic natural products, we tested various machine learning algorithms and selected random forest as a model for predicting the targeting activity of compounds. Lead compounds were then subjected to virtual screening and covalent docking, integrated absorption, distribution, metabolism and excretion (ADME) testing, and structure-based pharmacophore model validation to select the most suitable compounds. Finally, we performed molecular dynamics simulations to verify the binding mode of the lead compound to KRAS. The lazypredict function package was initially used, and the Accuracy score and F1 score of the random forest algorithm exceeded 60%, which can be considered to carry a strong ability to distinguish the data. Four marine natural products were obtained through machine learning identification and covalent docking screening. Compound and compound were selected for further validation after ADME and toxicity studies, and pharmacophore analysis indicated that they had a favorable pharmacodynamic profile. Comparison with the positive control showed that they stabilized switch I and switch II, and like MRTX849, retained a novel binding mechanism at the molecular level. Molecular dynamics analysis showed that they maintained a stable conformation with the target protein, so compound and compound may be effective inhibitors of the G12C mutant. These findings reveal that the mangrove-derived secondary metabolite compound and compound might be potential therapeutic agents for KRAS.

摘要

红树林次生代谢产物具有许多独特的生物活性。我们在其中鉴定出了可能靶向KRAS的先导化合物,KRAS被认为与多种癌症密切相关。目前正在开发多种直接靶向KRAS的新型小分子,包括针对KRAS突变体的共价变构抑制剂、结合在开关I/II口袋或A59位点的蛋白质-蛋白质相互作用抑制剂,以及靶向核苷酸结合位点的GTP竞争性抑制剂。为了确定红树林次生代谢天然产物的候选库,我们测试了各种机器学习算法,并选择随机森林作为预测化合物靶向活性的模型。然后对先导化合物进行虚拟筛选和共价对接、整合吸收、分布、代谢和排泄(ADME)测试,以及基于结构的药效团模型验证,以选择最合适的化合物。最后,我们进行了分子动力学模拟,以验证先导化合物与KRAS的结合模式。最初使用了lazypredict函数包,随机森林算法的准确率得分和F1得分超过60%,可以认为具有很强的数据区分能力。通过机器学习鉴定和共价对接筛选获得了四种海洋天然产物。在进行ADME和毒性研究后,选择化合物 和化合物 进行进一步验证,药效团分析表明它们具有良好的药效学特征。与阳性对照相比,它们稳定了开关I和开关II,并且与MRTX849一样,在分子水平上保留了一种新的结合机制。分子动力学分析表明它们与靶蛋白保持稳定构象,因此化合物 和化合物 可能是G12C突变体的有效抑制剂。这些发现表明,源自红树林的次生代谢产物化合物 和化合物 可能是KRAS的潜在治疗剂。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9455/9146975/a7590e07fda8/pharmaceuticals-15-00584-g001.jpg

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验